README.md

In compbiomed/curatedTBData: Curation of existing tuberculosis transcriptomic studies

curatedTBData

The curatedTBData package collects 49 transcriptomic studies, with ongoing additions, focusing on patients with tuberculosis (TB) and other clinical conditions.

Installation

curatedTBData is now available on Bioconductor. You can install the package via:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("curatedTBData")

To install the development version:

install.packages("devtools") 
devtools::install_github("xutao-wang/curatedTBData")

Load Data

View summarized table for all the available data:

data("DataSummary", package = "curatedTBData")
View(DataSummary)

Load studies:

library(curatedTBData)

# List of all available resources with dryrun = TRUE
curatedTBData("", dryrun = TRUE)

# Load full version of single study
curatedTBData("GSE39939", dryrun = FALSE, curated.only = FALSE)

# Load curated version of multiple studies
curatedTBData(c("GSE39939","GSE107993"), dryrun = FALSE, curated.only = TRUE)

compbiomed/curatedTBData documentation built on March 14, 2024, 2:08 p.m.